Nicola Soranzo
99e352a3d0
Merge branch 'release_25.0' into dev
2025-06-22 15:26:46 +01:00
Nicola Soranzo
1cc2d6e5e6
Merge branch 'release_24.2' into release_25.0
2025-06-22 12:56:24 +01:00
Nicola Soranzo
414019da34
Fix docs versioning
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for Galaxy releases (e.g. 24.2 and 25.0) that have only tags with
2 dots.
2025-06-21 20:16:29 +01:00
Nate Coraor
96523d4570
Merge remote-tracking branch 'upstream/release_25.0' into dev
2025-06-20 16:18:47 -04:00
Marius van den Beek
e95a55907f
Merge pull request #20516 from natefoo/web-client-static-fixes
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[25.0] Fixes for static handling and the web_client package
2025-06-19 11:18:23 +02:00
mvdbeek
cafd0c8c62
Merge branch 'release_25.0' into dev
2025-06-19 10:18:46 +02:00
mvdbeek
39285ff347
Run make config-rebuild
2025-06-19 09:44:39 +02:00
Björn Grüning
af684f2993
fix link in user release notes
2025-06-19 08:33:56 +02:00
Ahmed Awan
3000e4343d
Merge branch 'release_25.0' into dev
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# Conflicts:
# lib/galaxy/version.py
# packages/app/HISTORY.rst
# packages/auth/HISTORY.rst
# packages/config/HISTORY.rst
# packages/data/HISTORY.rst
# packages/files/HISTORY.rst
# packages/job_execution/HISTORY.rst
# packages/job_metrics/HISTORY.rst
# packages/meta/HISTORY.rst
# packages/navigation/HISTORY.rst
# packages/objectstore/HISTORY.rst
# packages/schema/HISTORY.rst
# packages/selenium/HISTORY.rst
# packages/test_api/HISTORY.rst
# packages/test_base/HISTORY.rst
# packages/test_driver/HISTORY.rst
# packages/tool_shed/HISTORY.rst
# packages/tool_util/HISTORY.rst
# packages/tours/HISTORY.rst
# packages/util/HISTORY.rst
# packages/web_apps/HISTORY.rst
# packages/web_framework/HISTORY.rst
# packages/web_stack/HISTORY.rst
2025-06-18 12:00:07 -05:00
Ahmed Awan
404e34ce42
fix natalie's github username
2025-06-17 15:30:48 -05:00
Ahmed Hamid Awan and José Manuel Domínguez
bcac9bcc10
Update doc/source/releases/25.0_announce.rst
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Co-authored-by: José Manuel Domínguez <43052541+kysrpex@users.noreply.github.com >
2025-06-17 15:18:16 -05:00
Ahmed Awan
7be1f9e3bd
remove developer section
2025-06-17 15:17:47 -05:00
Ahmed Awan
9f34683d11
add final PRs to release notes
2025-06-17 15:16:12 -05:00
Ahmed Awan
f364304e7e
replace youtube video with latest one for preferred viz display
2025-06-17 14:52:08 -05:00
Ahmed Awan
f16f4e67ed
add latest PRs 06/12
2025-06-17 14:52:08 -05:00
Ahmed Awan
95834d14a4
add communications section
2025-06-17 14:52:08 -05:00
Ahmed Hamid Awan and José Manuel Domínguez
d841082b81
add eLabFTW and RSpace integrations to release notes
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TODO: Update the blog post URL for RSpace once we publish these notes
Co-authored-by: José Manuel Domínguez <43052541+kysrpex@users.noreply.github.com >
2025-06-17 14:52:08 -05:00
Ahmed Awan
090f258d15
add a 24.2 targeting PR which we missed
2025-06-17 14:52:08 -05:00
Ahmed Awan
4b9d28b96e
add latest PRs 06/11
2025-06-17 14:52:08 -05:00
Ahmed Awan and John Davis
9d9767454b
add links for BRC and IWC to release notes highlight
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Co-authored-by: John Davis <jdavcs@gmail.com >
2025-06-17 14:52:08 -05:00
Ahmed Awan and Nicola Soranzo
25912ae869
deprecate ToolDocumentCache in release notes
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-06-17 14:52:08 -05:00
Ahmed Awan
2a6fe21528
add JD as co-manager
2025-06-17 14:52:08 -05:00
6b22b39514
improve wording in user facing notes
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Co-authored-by: John Davis <jdavcs@gmail.com >
Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2025-06-17 14:52:08 -05:00
Ahmed Hamid Awan and David López
dc81ca9a57
Update doc/source/releases/25.0_announce_user.rst
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Co-authored-by: David López <46503462+davelopez@users.noreply.github.com >
2025-06-17 14:52:08 -05:00
Ahmed Awan and Nicola Soranzo
5447292292
move current Deprecation Notices to Admin Notes
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As these are actual removals not deprecations.
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-06-17 14:52:08 -05:00
Ahmed Awan
51a1456957
add deprecation notices
2025-06-17 14:52:08 -05:00
Ahmed Awan
b208eaa675
add latest PRs 06/09
2025-06-17 14:52:08 -05:00
Ahmed Awan
78093458f6
finalize release notes highlights
2025-06-17 14:52:08 -05:00
Ahmed Awan
1ba2080877
finalize 2 more highlights, reorganize by youtube videos first
2025-06-17 14:52:08 -05:00
Ahmed Awan
556baadcd6
remove a highlight
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A very cool enhancement showcased in several features this release, but highlighting it itself is maybe not needed for user facing release notes; a very resuable component hence, more dev focused?
2025-06-17 14:52:08 -05:00
Ahmed Awan
1a9e7fc017
finalize more highlights, adjust others, format spacing better
2025-06-17 14:52:08 -05:00
Ahmed Awan
0bfb4c049f
finalize 2 more highlights
2025-06-17 14:52:08 -05:00
Ahmed Awan
26ee920d3b
Add config changes to release notes
2025-06-17 14:52:08 -05:00
Ahmed Awan
85b58b1a93
add highlights to release notes, finalize 3 highlights, remaining draft
2025-06-17 14:52:08 -05:00
Ahmed Awan
92c3065314
Add 25.0 to releases docs index page
2025-06-17 14:52:08 -05:00
Ahmed Awan
194f4df71d
25.0 release notes
2025-06-17 14:52:07 -05:00
Charles Coulombe and Nicola Soranzo
03b2bb539f
Update doc/source/admin/special_topics/mulled_containers.rst
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-06-12 13:50:32 -04:00
Charles Coulombe and Nicola Soranzo
1270fdd64b
Update doc/source/admin/special_topics/mulled_containers.rst
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2025-06-12 13:50:22 -04:00
Charles Coulombe
e646c85ef9
Update mulled_containers.rst
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Fixed typo
2025-06-12 11:07:32 -04:00
Nicola Soranzo
0b2e2f4307
Deprecate `enable_tool_document_cache`
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See https://github.com/galaxyproject/galaxy/issues/20432 .
2025-06-10 19:57:53 +01:00
mvdbeek
f311f7d334
Add basic documentation for admins
2025-05-12 10:54:56 +02:00
John Chilton
219796f049
Implement paired_or_unpaired collections, list wizards.
2025-05-09 17:39:38 -04:00
Marius van den Beek
2eac17db1e
Merge pull request #19936 from jdavcs/dev_13922_metrics
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Drop old job metrics
2025-05-09 15:02:21 +02:00
John Davis
b05170ef7c
Add warning, gxadmin script ref to script, docs
2025-05-09 12:19:16 +02:00
John Davis
26cff176bf
Add documentation
2025-05-09 12:19:15 +02:00
davelopez
5347684565
Fix isort linting
2025-05-09 12:14:20 +02:00
José Manuel Domínguez
10de12c5f1
Implement file source to integrate Galaxy with RSpace
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This commit implements a FilesSource that interacts with an RSpace [1] instance and includes a file source template so that users can define their own file sources based on it.
RSpace is an electronic lab notebook
(ELN) designed for documenting, managing and sharing scientific data. The central concepts in RSpace are the Workspace,
the Inventory and the Gallery.
The Workspace's role is organizing and managing research activities. It allows creating documents, folders and research
notebooks [2]. The Inventory is a tool to keep track of laboratory resources, such as reagents, samples and equipment
[3]. The Gallery is where any research data represented as files is stored [4].
The FilesSource implemented by this module accesses the Gallery of an RSpace instance. The Gallery is organized in
categories (e.g. Images, Audio, Documents, Chemistry), where each category is itself a tree structure with folders and
files just like a regular filesystem, although there is a key difference: categories and their subfolders can only
contain files of certain types (e.g. jpeg, bmp, png, etc. for the Images category).
This implementation is based on the rspace-client-python` library [5], which provides a PyFilesystem2 [6] interface
to interact with RSpace's Gallery (available as `GalleryFilesystem` in the rspace_client.eln.fs` module). It
consists just of a minimal wrapper (based on the base `PyFilesystem2FilesSource` provided by Galaxy) around the
`GalleryFilesystem` class.
References:
- [1] https://www.researchspace.com/
- [2] https://documentation.researchspace.com/article/bzgr8ea9e3-the-workspace
- [3] https://documentation.researchspace.com/category/zpizk20kgx-inventory
- [4] https://documentation.researchspace.com/article/sl6mo1i9do-the-gallery
- [5] https://github.com/rspace-os/rspace-client-python
- [6] https://docs.pyfilesystem.org/
2025-05-09 12:04:46 +02:00
Marius van den Beek
12f7449459
Merge pull request #19390 from jmchilton/tags
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Documentation around highlighting PRs for release notes.
2025-05-09 09:34:45 +02:00
Dannon Baker
e8cfa1cb0f
Merge remote-tracking branch 'upstream/dev' into tool-install-opt
2025-05-08 17:26:39 -04:00
Nate Coraor
decf037cd3
Support setting and displaying timezone with the core metrics plugin
2025-05-06 11:45:51 -04:00
Nicola Soranzo